Merge branch 'main' of https://github.com/mvapontes/KEGGAPI.jl

.github/workflows/CI.yml

@@ -25,7 +25,7 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
@@ -44,7 +44,7 @@ jobs:
       contents: write
       statuses: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'

docs/src/index.md

@@ -6,11 +6,16 @@ CurrentModule = KEGGAPI
 
 Documentation for [KEGGAPI](https://github.com/bwbioinfo/KEGGAPI.jl).
 
-```@index
+[KEGG](https://www.genome.jp/kegg/)
+
+```@contents
+Pages = [
+    "man/functions.md",
+    "man/examples.md",
+]
+Depth = 2
 ```
 
-## Functions
 
-```@autodocs
-Modules = [KEGGAPI]
-```
+```@index
+```

docs/src/man/examples.md

@@ -0,0 +1,54 @@
+# Some Examples
+
+## Basics
+
+Examples analogous to [KEGG Conv](https://www.kegg.jp/kegg/rest/keggapi.html#conv)
+
+Querying the API for a simple conversion:
+
+```@example
+using KEGGAPI
+output = KEGGAPI.conv("eco", "ncbi-geneid"); 
+```
+
+Outputs a list with
+1. The API call
+2. The column headers of the call ( if the result is tabular )
+3. The data
+
+This allows to easily convert to a data frame:
+
+```@example
+using DataFrames
+DataFrame(
+  output.data,
+  output.colnames
+)
+```
+
+```@example
+using KEGGAPI
+output = KEGGAPI.conv("ncbi-geneid", "eco");
+DataFrame(
+  output.data,
+  output.colnames
+)
+```
+
+```@example
+using KEGGAPI
+output = KEGGAPI.conv("ncbi-proteinid", "hsa:10458+ece:Z5100");
+DataFrame(
+  output.data,
+  output.colnames
+)
+```
+
+```@example
+using KEGGAPI
+output = KEGGAPI.conv("genes", "ncbi-geneid:948364");
+DataFrame(
+  output.data,
+  output.colnames
+)
+```

docs/src/man/functions.md

@@ -0,0 +1,5 @@
+# KEGGAPI.jl Functions
+
+```@autodocs
+Modules = [KEGGAPI]
+```

src/Conv.jl

@@ -4,12 +4,14 @@ KEGGAPI.conv(<target_db>, <source_db>)
 
 Convert KEGG identifiers to/from outside identifiers.
 
-# Examples
-```julia-repl
+Example:
+
+```@example
+using KEGGAPI
 KEGGAPI.conv("eco", "ncbi-geneid")
 KEGGAPI.conv("ncbi-geneid", "eco")
-KEGGAPI.conv("hsa:10458+ece:Z5100", "ncbi-proteinid")
-KEGGAPI.conv("ncbi-geneid:948364", "genes")
+KEGGAPI.conv("ncbi-proteinid", "hsa:10458+ece:Z5100")
+KEGGAPI.conv("genes", "ncbi-geneid:948364")
 ```
 """
 function conv(target_db::String, source_db::String)

src/Find.jl

@@ -4,8 +4,8 @@ KEGGAPI.find(database, query) -> KeggTupleList
 
 Find entries in a specific database from the KEGG API.
 
-# Examples
-```julia-repl
+```@example
+using KEGGAPI
 KEGGAPI.find("compound","glucose")
 ```
 """

src/Get.jl

@@ -8,16 +8,19 @@ and returns a vector containing the urls used and the data returned.
 The get function will split the vector into groups of 10 and make a request for each chunk.
 
 # Examples
-```julia-repl
+```@example
+using KEGGAPI
 kegg_get_genes = 
     KEGGAPI.kegg_get(
         ["hsa:10458", "hsa:10458", "hsa:10458", "hsa:10458"], 
         "ntseq"
-        )
+        );
+first(kegg_get_genes)
 kegg_get_compounds = 
 KEGGAPI.kegg_get(
     ["C01290","G00092"]
-    )
+    );
+first(kegg_get_compounds)
 ```
 """
 function kegg_get(query::Vector{String}, option::String = "")

src/Images.jl

@@ -3,8 +3,9 @@ KEGGAPI.get_image(pathway) -> Image
 
 Get an image of a specific pathway from the KEGG API.
 
-# Examples
-```julia-repl
+Example:
+
+```@example
 KEGGAPI.get_image("hsa00010")
 ```
 """
@@ -20,7 +21,7 @@ KEGGAPI.save_image(image, filename) -> filename
 Save an image to a file.
 
 # Examples
-```julia-repl
+```example
 image = KEGGAPI.get_image("hsa00010")
 KEGGAPI.save_image(image, "glycolysis.png")
 ```

src/Info.jl

@@ -3,8 +3,9 @@ KEGGAPI.info(database) -> String
 
 Get information about a specific database from the KEGG API.
 
-# Examples
-```julia-repl
+Example:
+
+```example
 KEGGAPI.info("kegg")
 ```
 """

src/Link.jl

@@ -4,8 +4,9 @@ KEGGAPI.conv(<target_db>, <source_db>)
 
 Find related entries by using database cross-references
 
-# Examples
-```julia-repl
+Example:
+
+```example
 KEGGAPI.link("pathway", "hsa")
 ```
 """

src/List.jl

@@ -4,8 +4,9 @@ KEGGAPI.list(database)
 
 Get a list of entries from a specific database from the KEGG API.
 
-# Examples
-```julia-repl
+Example:
+
+```example
 KEGGAPI.list("pathway")
 ```
 """